VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Nov 19 2008 - 00:23:56 CST

The value given is just an example, you should take it with a grain of salt.
(hahaha) There is not a default value; you either must give a
concentration or a fixed number of ions.

 

The autoionize gui plugin has an option to only neutralize the system;
alternatively, you could just specify -is .0001 to make it only place enough
ions to neutralize the system and no more (assuming this is what you want to
do). Physiological concentrations are definitely higher than 50 mM, more
like 150 mM, I think, although the relevant ion species and concentrations
vary so consider the native environment of your system carefully. Keep in
mind though that the concentration in the autoionize plugin is effectively
twice that in experiments (i.e. 150mM KCl in experiment -> 300mM total ion
concentration (K+ and Cl-) in autoionize).

 

 

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Rabab Toubar
Sent: Tuesday, November 18, 2008 7:40 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Autoionize plugin

 

Hi all,

 

1- I was wondering what is the importanced of the ionic concentration in the
mentioned script at this webpage:
http://www.ks.uiuc.edu/Research/vmd/plugins/autoionize/

 

autoionize -psf file.psf -pdb file.pdb -is 0.05

 

Is it to resemble the physiological pH? What if I didn't include it in the
script, is there a default value for it?

 

2- Which would be more accurate: calculating the net charge on the peptide
and specifying the number of opposiite charge to neutralize it - provided it
is reasonably small, or using the autoionize

 

Thanks

Rabab